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Contents
1. Basics ................................................................................................................................................................................................................. 2
DNA.......................................................................................................................................................................................................................... 2
RNA .......................................................................................................................................................................................................................... 2
GENOME SEQUENCING ............................................................................................................................................................................. 3
1.2 Protein synthesis ...................................................................................................................................................................................... 3
Transcription ..................................................................................................................................................................................................... 3
Translation .......................................................................................................................................................................................................... 3
Recombinant DNA technology ..................................................................................................................................................................... 4
2. Gene editing .................................................................................................................................................................................................. 5
How gene editing is done ...................................................................................................................................................................... 6
Genome Editing Techniques .................................................................................................................................................................... 6
CRISPR-cas9 technology ............................................................................................................................................................................ 7
Types of gene editing .................................................................................................................................................................................... 7
Types of cells (from perspective of Gene editing) ............................................................................................................................ 7
Gene therapy ..................................................................................................................................................................................................... 9
GM crops .............................................................................................................................................................................................................. 9
Animal cloning ....................................................................................................................................................................................................... 9
3- Parent baby .................................................................................................................................................................................................11
GM crops in India ..........................................................................................................................................................................................13
Stem cells ................................................................................................................................................................................................................13
Stem cell therapy ...........................................................................................................................................................................................14
3. Virus, Infection and Immune system ............................................................................................................................................15
How a virus infects the body? ................................................................................................................................................................15
Immunity ............................................................................................................................................................................................................15
Rapid antigen test for COVID .................................................................................................................................................................16
PCR reaction (RT PCR Test - Reverse Transcription-Polymerase Chain Reaction)...............................................17

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1. Basics
DNA
 Nucleic acid present in all organism: in the form of DNA and RNA.
 The structure of DNA defines the basic genetic makeup of the body.
 It carries and transmits the hereditary material/genetic instruction from parents their generation.
 Works for production of proteins.
 Structure of DNA
o The DNA molecule consists of two strands that wind around one another to form a shape known as a
double helix.
o Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate groups.
o Attached to each sugar is one of four bases--adenine (A), cytosine (C), guanine (G), and thymine (T).
o The two strands are held together by bonds between the bases; adenine bonds with thymine, and
cytosine bonds with guanine.

 Application of DNA-
o Solving crimes
o Identifying human remains
o Testing for paternity
o Genetic testing.
o Develops genetically transformed plants.
RNA
 Structure of RNA
o RNA consists of ribose nucleotides (nitrogenous bases appended to a ribose sugar) attached by
phosphodiester bonds, forming strands of various lengths.
o The nitrogenous bases in RNA are adenine, guanine, cytosine, and uracil, which replaces thymine in DNA.

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 Utility of RNA
o Helps in synthesis of protein in our body.
o Production of new cells in human body.
o Translation of DNA into proteins.
o Messenger between ribosome and the DNA.
 Types of RNA
o tRNA (transfer RNA)- choose the right protein required by the body , which then helps the ribosomes.
o rRNA (ribosomal RNA)- synthesis and translation of m RNA into proteins.
o mRNA ( messenger RNA)-transfers the genetic material to ribosomes and pass the instructions about
the type proteins, necessary for blood cells.
o Genome: A genome is the complete set of genetic information in an organism. It provides all of the
information the organism requires to function.
o Transcriptome: The term "transcriptome" can also be used to describe the array of mRNA transcripts
produced in a particular cell or tissue type. So a transcriptome is the full range of messenger RNA, or
mRNA, molecules expressed by an organism.

GENOME SEQUENCING
 All living things (bacteria, plants, and mammals) have a distinct genetic code, or genome, made up of
nucleotide bases (A, T, C, and G). An organism's own DNA fingerprint, or pattern, can be detected if you know
the bases' sequence.
 Sequencing is the process of establishing the order of bases. An organism's genome's base order can be
determined in one step via a laboratory approach called whole genome sequencing.

1.2 Protein synthesis


 Protein synthesis is the process in which cells make proteins. It occurs in two stages: transcription and
translation.

Transcription
o It is the transfer of genetic instructions in DNA to mRNA in the nucleus.
o After the mRNA is processed, it carries the instructions to a ribosome in the cytoplasm.
o Thus, transcription is regarded as the first step of gene expression.

Translation
o Translation occurs at the ribosome, which consists of rRNA and proteins
o The instructions in mRNA are read, and tRNA brings the correct sequence of amino acids to the ribosome.
o Then, rRNA helps bonds form between the amino acids, producing a polypeptide chain.
o After a polypeptide chain is synthesized, it may undergo additional processing to form the finished
protein.

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Recombinant DNA technology


Recombinant DNA (rDNA) is a technology that uses enzymes to cut paste together DNA sequence of interest. The
recombinant DNA sequence can be placed into vehicle called vectors that ferry the DNA into a suitable host cell
where it can be copied or expressed.

Tools involved in Recombinant DNA technology


 Restriction Enzymes:
o Restriction enzymes belong to a larger class of enzymes called nucleases.
o These are of two kinds; exonucleases and endo-nucleases.

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o Exonucleases remove nucleotides from the ends of the DNA whereas endonucleases make cuts at specific
positions within the DNA.
o Restriction endonucleases are used in genetic engineering to form 'recombinant' molecules of DNA,
which are composed of DNA from different so urces/genomes.

 Separating DNA molecules:


o The most common separation technique used is gel electrophoresis.
o This technique takes advantage of the negative charge on DNA molecules by using an electrical field to
provide the force necessary to separate DNA molecules based on size.
o The separated DNA fragments can be visualised only after staining the DNA with a compound known as
ethidium bromide followed by exposure to UV radiation.

 Methods of INSERTION OF rDNA in Host Cells


o Micro-injection: Recombinant DNA is directly injected into the nucleus of an animal cell.
o Biolistics or gene gun: Cells are bombarded with high velocity micro-particles of gold or tungsten coated
with DNA in a method known as biolistic or gene gun.
o This method is suitable for plants

Steps involved in process are:


1. Isolation of genetic material: it is to isolate the desired DNA in its pure form I.e. free from other
macromolecules.
2. Restriction enzyme digestion: restriction enzymes act molecular scissors that cut DNA at specific
locations. These reaction are called restriction enzyme digestion.
3. Amplification using PCR: polymerase chain reaction or PCR is a method of making multiple copies of a DNA
sequence using the enzyme z-DNA polymerase in vitro.
4. Ligation of DNA molecules: the process of joining two pieces together using the enzyme DNA ligase is a
ligation.
 The resulting DNA molecules is a hybrid of two DNA molecules

Hence this new hybrid DNA is also called a rDNA molecule and technology is referred as
recombinant DNA technology.
5. Insertion of recombinant DNA into host
6. Isolation of recombinant cells.
Applications-
 Disease diagnosis- used to detect the presence of HIV in a person.
 Food and agriculture- manufacture of GM crops and climate resilient crop.
 Medicines- production of insulin.
 Gene therapy- it is used an attempt to correct the gene defects which give rise to hereditary diseases.
 Development of vaccines and recombinant hormones.
2. Gene editing
Biotechnology
 deals with techniques of using live organisms or enzymes from organisms to produce products and processes
useful to humans.
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The two core techniques that enabled birth of modern biotechnology are:
 Genetic engineering: Techniques to alter the chemistry of genetic material (DNA and RNA) to introduce these
into host organisms and thus change the phenotype of the host organism.
 Bioprocess engineering: Maintenance of sterile (microbial contamination-free) ambience in chemical
engineering processes to enable growth of only the desired microbe/eukaryotic cell in large quantities for
the manufacture of biotechnological products like antibiotics, vaccines, enzymes, etc.

 It is a process of changing an
organism’s DNA. Using this genetic
material is added, removed or
altered at specific location in the
genome.
How gene editing is done
 Enzymes which cut DNA are known
as engineered nucleases.
 It is performed using enzymes,
particularly nucleases whose
purpose is to target a specific DNA
sequence, where they introduce
cuts into the DNA strands which
enables the removal of existing DNA
and the insertion of replacement DNA.
Applications-
1. Treating inherited diseases sickle cell anemia
2. Helps to understand what specific genes do.
3. Prevents inheritance of genetic diseases.
4. Generates more resilient crops.
5. Detecting species in environment.

Genome Editing Techniques


The core technologies now most used to facilitate genome editing, are :
 Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9):
o CRISPR is the DNA-targeting component of the system, and it is made up of an RNA molecule, or
'guide,' that is engineered to attach to certain DNA bases via complementary base-pairing.
o CRISPR-associated protein 9 (Cas9) is the nuclease component that cuts the DNA.
o The CRISPR-Cas9 genetic scissors were discovered by Emmanuelle Charpentier and Jennifer A. Do
udna, who won the Nobel Prize in Chemistry in 2020
 Transcription activator-like effector nucleases (TALENs):
o Transcription activator-like effector (TALE) domains make up the DNA-binding domain of TALENs.
o The nuclease portion of TALENs, like ZFNs. is usually a FokI nuclease.
 Zinc-finger nucleases (ZFNs):

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o ZFNs are fusions between a custom-designed Cyst-His2 zinc-finger protein and the cleavage domain
of the FokI restriction endonuclease.
o FokI cleavage domain, which cuts DNA within a five-to seven-bp spacer sequence that separates two
flanking zinc-finger binding sites.
 Homing endonucleases or mega nucleases:
o Homing endonucleases, also known as mega nucleases.
o These enzymes make extensive sequence-specific contacts with their DNA substrate.
o However, unlike ZFNs and TALENs, the binding and cleavage domains in homing endonucleases are
not modular.
o This overlap in form and function makes their repurposing challenging, and limits their utility for more
routine applications of genome editing.

CRISPR-cas9 technology
 It is part of adaptive immunity system used by
bacterial cells to recognize and destroy viral
DNA.
 CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats): They are sections
of DNA, containing short repetitions of base
sequences followed by spacer DNA segments.
 CAS-9 (CRISPR-associated protein 9): It is an
enzyme. It relies on guide RNA to find the DNA
sequence of interest. It will then introduce a
double strand break at a specific location
within a strand of DNA.

Types of gene editing


 Germline editing: genome of an individual is
edited in a way that the change is heritable.
This is achieved through genetic alterations
within the germ cells, or the reproductive cells, such as the egg and sperm.
 Somatic cell gene editing: introduction of genes into bone marrow cells, blood cells, skin cells that will not
be inherited later generations.

Types of cells (from perspective of Gene editing)


Somatic cells Stem cell Reproductive cell
 Somatic cells are diploid  Stem cells are body’s  A cell whose nucleus unites with that
cells, which contain two raw material, i.e. cells of a cell of the opposite sex to form a
pairs of chromosomes, from which all other new organism reproductive cell.
one received from each cells with specialized  Gametes are an organism's
parent. functions are generated. reproductive cells sex cells.

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 Any cell other than germ  They can divide through  Female gametes are called ova or egg
cells (sperm and egg), mitosis single cell cells, and male gametes are called
gametocytes (cells that divided into two sperm.
divide to form germ identical daughter cells.  Gametes these are haploid cells,
cells), and  Limitlessly to replenish and each cell carries only one copy of
undifferentiated stem other cell types of each chromosome.
cells are known as multi-cellular  Gamete is capable of fusing with
somatic cells. organisms throughout another haploid reproductive cell to
 Somatic cells are not their life. form a diploid zygote. The zygote is
capable of producing  After stem cell division, formed by the fusion (or combining)
offspring. But, they form each newly produced of two gametes, i.e. male gamete and
all the internal organs cell can either remain as female gamete. This union of gametes
and tissues and a stem cell or resulting in a zygote is called
contribute to their differentiate to form any fertilization.
functionalities. other cell type with  These reproductive cells are
 They are responsible for more defined functions, produced through meiosis.
growth, repair and such as muscle cell,
regeneration. blood cell, or neural cell.
 Some of the specialized  Types of stem cells:
somatic cells are: - Embryonic Stem
- Skin cells Cells.
- Muscle cells - Embryonic germ
- Nerve cells cells.
- Blood cells. - Adult Stem Cells.
 Application –
- Treatment of brain
diseases.
- Treatment of blood
diseases.
- Treatment of
cardiovascular.
- Tissue regeneration.

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Gene therapy
 It is a therapy that uses genes to
prevent diseases.
 It might allow doctors to treat a
disorder by inserting a gene into
a patients cells instead of using
drugs or surgery.
 Types of gene therapy- somatic
cell gene therapy and germline
gene therapy.
 Advantages
o Gene therapy has the
potential to eliminate
and prevent hereditary
disease.
o It is possible to cure
heart diseases, cancer
and AIDS.
o It can be used to discard diseases from the future generation.
GM crops
 Genetically modified plants/crops using genetic engineering methods.
 Crops are genetically modified in order to introduce a trait with one of these properties –
o To increase the nutritional content, which the soil cannot provide.
o To increase the crop yield.
o Make them resistant to harsh atmospheric /environmental conditions such as high/low temperature,
salinity.
o To make them insect resistant.
Animal cloning
Cloning – it is the process of generating identical copy of a cell or an organism.
Animal cloning
 Procedure of creating a whole new multi-cellular organism which is genetically identical to original
organism.
 Non-sexual process
 No fertilization or inter-gamete contact takes place.

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Different levels of cloning

 Molecular cloning
- Isolation of DNA sequence from any species (often a gene) in its insertion into a vector (host bacterium)
for propagation without alteration.
 Cellular cloning
- Copies of cells are made resulting in the formation of identical cells from a single cell. This type of
cloning is used in stem cell research.
 Organism cloning.
- A multi-cellular organism is created, genetically identical to other organism.
Types of cloning
 Gene cloning
- It creates copies of genes or segments of DNA.
 Reproductive cloning
- It involves the implantation of a cloned embryo into a real or an artificial uterus. The embryo develops
into a fetus that is genetically identical to the donor of the original nucleus.

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 Therapeutic/ biomedical cloning


- It is used to clone embryos for the purpose of extracting stem cells for use in replacing or repairing
damaged tissues or organs, achieved by transferring a diploid nucleus from a body cell into an egg
whose nucleus has been removed.
Applications of cloning-
 Biomedical- disease models, bioreactors.
 Agricultural –
- can be used to create copies of animals with highly valued traits, like dairy cow with high milk
production
- Livestock improvement
- Genetic improvement
- Conservation of endangered species.
 Research
- Stem cell research
- Understanding embryology.
Criticism
 Cloning contradicts natural reproductive process and hence has its negative effects-
 Sometimes a clone is not able to perform metabolic process like eating, drinking, etc.
 Clone may have short life span.
 They can experience developmental anomalies.
 Reproductive cloning is considered unnatural by some and hence it can violate religious belief.

First cloning of a sheep (dolly)


Feb 1997, Ian Wilmut and his colleagues at the Roslin institute, successfully cloned a sheep, from the
mammary glands of an adult female. Dolly was the first mammal to be effectively cloned from an adult cell.
She was cloned at Scotland lived and died there only.

3- Parent baby
 A baby in which the vast majority of nuclear DNA comes from the mother and the father and a small amount
of mitochondrial DNA comes from a female donor.
 This reproductive technology focuses on reducing the effects of mutations that occur in the DNA of
mitochondria, which reside in cytoplasm. This could prevent the transmission to their offspring of
mitochondria diseases.
 There are two main techniques involved:

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 Mitochondrial spindle transfer:


o Inside laboratory,
scientists remove the
nucleus from a healthy
donor egg and replace it
with a nucleus taken
from the egg cell of a
woman who carries a
rare neurological disease
called Leigh syndrome.
o This leaves the donor’s
healthy mitochondria
intact. The scientists
then fertilize the
modified egg with the
father’s sperm.
o After this the 'reconstructed embryo' is implanted into the mother’s uterus.

 Pronuclear transfer:
o At the time of fertilization,
genetic material is fused.
One set comes from the
egg and another comes
from dad’s sperm.
o At early stage in
development, the two (egg
and sperm) have not yet
fused into a single
nucleus. This is called
Pronuclei.
o Pronuclei is the central,
DNA-containing parts of
fertilized eggs.
o In this technique
researchers fertilize the mother mouse’s egg and a donor egg at the same time. The pronuclei are
removed from the donor’s fertilized egg and discarded. These are then transferred to an egg cell
containing a healthy mitochondria.

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GM crops in India
BT COTTON
o MAHYCO: Maharashtra hybrid
corporation released first cotton
hybrid MECH1 in 1989.
o BT COTTON was the first genetically
modified crop which got commercially
accepted in 2002.
o It is developed with resistance to the
pink bollworm pest.
o Done by genes (cry1Ab and cry2Bc)
inserted from bacterium bacillus
thuringiensis (Bt).
 HTBT COTTON
o Herbicide resistant BT cotton.
o Inserted with ‘Cp4-Epsps’ from soil
bacterium, agro bacterium
tumefaciens glyphosate (modified
protein)makes it herbicide resistant.
o Not legal in India.

Bt BRINJAL
o Modified by inserting a gene from the
soil bacterium BT which has insecticidal property.
o The gene leads to dysfunction of the digestive system of insects who feeds on the crop. And hence they die.
o Developed by Maharashtra hybrid Seeds Company.
o Grown majorly in Andhra Pradesh, Madhya Pradesh, Tamil nadu.
*only GM COTTON is allowed presently in India.

Stem cells
 Cells are usually of two types- differentiated and undifferentiated.
 Differentiated cells- these are specialized cells to perform a unique function in the body.
 Undifferentiated cells- these are responsible for replenishing old, injured or dead cells.
 Stem cells are undifferentiated cells with the capacity to both differentiate and multiply into the 200 cells
type that form a human being.
 There are two categories of stem cells –adult stem cells and embryonic stem cells.
 Embryonic stem cells-
1. Found in the three germ layer of the embryo.
2. Inner cell mass of the embryo contains embryonic stem cells
3. Embryonic stem cells are the most potent, as their job is to become every type of cell in the body.
The full classification includes:

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 Totipotent: These stem cells can differentiate into all possible cell types. The first few cells
that appear as the zygote starts to
divide are totipotent.
 Pluripotent: These cells can turn into
almost any cell. Cells from the early
embryo are pluripotent.
 Multipotent: These cells can
differentiate into a closely related
family of cells. Adult hematopoietic
stem cells, for example, can become
red and white blood cells or platelets.
 Oligopotent: These can differentiate
into a few different cell types. Adult
lymphoid or myeloid stem cells can do
this.
 Embryonic stem cells are considered pluripotent instead of totipotent because they cannot
become part of the extra-embryonic membranes or the placenta.

 Adult stem cells


1. Found in differentiated tissues, but remain undifferentiated.
2. Stem cells in bone marrow are the most commonly studied type of cells.
3. Can be found in skeletal muscle, brain, blood, liver, and pancreas.

 Importance of stem cells


o To increase the understanding of how diseases may occur.
o To generate healthy cells to replace diseased cells.
o To test new drugs for safety and effectiveness.
Stem cell therapy
 It is the introduction of new adult stem cells into damaged tissue in order to treat an ailment or injury.
 The ability of stem cells to self-renew and give rise to different cells that can potentially replace diseased and
damaged areas in the body with minimal side effects.
 A number of stem cell therapies exist, but most are at experimental stages, costly or controversial.
 Any disease which involves tissue degeneration can be a potential disease for stem cell therapies. Some of
them are –
o Tissue repair
o Alzheimer’s disease.
o Heart disease
o Severe burns
o Diabetes
o Spinal cord injury
o Leukemia and cancer
o Rheumatoid arthritis.

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3. Virus, Infection and Immune system


 They cannot survive on their own, they need living cells to keep themselves alive.
 They reproduce inside the living cells called host. Unlike bacteria it can survive for only few hours without
the host.
 Enters the body through nose and mouth. Can also spread through contaminated blood, exchange of body
fluids or through sexual activities (Hepatitis C and HIV).
 Can be prevented through vaccines (Chicken pox, Measles and mumps.)
 Examples of infection: influenza, COVID-19 and common cold.
 Treatment: antiviral.
How a virus infects the body?
 Entry- the virus enters the body through the nose, mouth, eyes or the skin.
 Infects- once inside the body, a virus infects host cell by injecting its genetic material.
 Hijack protein formation machinery – the virus will hijack the cell in order to make many copies of it and to
hide from the immune system.
 Spread- the host cell dies as the virus multiplies and moves into more cells. This is when the body gets sick.
 Viruses are small pieces of RNA or DNA wrapped up in a layer of proteins, which protect the genetic material.
 They cannot survive on their own so they need a host cell. They replicate and create other viruses.
 It enters the body and adheres to the cell surface. It then seeks for cells in different parts of the body (liver,
respiratory system or blood.)
 When the virus is inside the cell, it will open up so that it’s RNA and DNA will come out and go straight to the
nucleus. They will enter a molecule, and make copies of the virus.
Immunity
 A large number of pathogenic (disease causing) microorganisms are present in the environment that
continuously interacts to our body.
 Immunity is the ability of the body to protect against all such types of foreign bodies like bacteria, virus, and
toxic substances etc. which enter
the body.
 Immunity is done by immune
system which is a complex
network of lymphoid organs such
as bone marrow, thymus, spleen
etc.
 Innate immunity
o It is also called natural and
native immunity, consist of
mechanism that exist before
infection and are capable of
rapid responses to microbes.
o Types of innate immunity
o Physical barrier- skin on our
body is the main physical
barrier which prevents entry of
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pathogens; mucus coating (epithelium) is present in gastrointestinal, respiratory tracts which trap the
microbes entering our body.
o Cellular barrier- at the cellular level, barriers consist of cells that are tightly held together to prevent
invaders from crossing through to deeper tissue.
o Physiological barrier- saliva in mouth, tears in eyes, acid in stomach.
Acquired immunity
 It is developed by the host in its body after exposure to suitable antigen. It is pathogen specific and is
characterized by memory.
 When a pathogen enters a body for the first time body produces a response primary response.
 When the body encounters the same pathogen again a highly intensified secondary/anamestic response is
observed.
 The primary and secondary immune response is carried out with the help of two special type of lymphocytes
present in our blood.
 Here, B-lymphocytes produce an army of protein in response to pathogens into our blood to fight with them.
T-lymphocytes do not secrete antibodies but help B-cells to produce them.
 These proteins are called antibodies.
 Types of acquired immunity
o Two types active and passive immunity.
o Active immunity: induced by natural exposure to a pathogen or by vaccination. Can be categorized into
two types- naturally acquired and artificially acquired active immunity.
o Passive immunity: it is achieved by transfer of immune products, such as antibody or sensitized T-cells,
from an immune individual to non-immune one. two types- naturally
o Acquired and artificially acquired passive immunity.
Rapid antigen test for COVID
 Rapid or fast COVID-19 test is a viral test, one of the two types of tests used to detect COVID-19.
 Rapid antigen tests are considered to be one of the simplest and quickest ways to test for COVID-19.
 Antigen any substance that the body recognizes as harmful or foreign, which induces the immune system
to produce antibodies against it.
 Rapid antigen tests identify protein fragments on the surface of the coronavirus to identify the presence of
the pathogen amongst people doing the test. Samples are taken from subjects by swabbing inside the nose or
mouth.
 procedure:
- Collect the sample by swabbing and rotating the cotton swab inside both nostril
- Place the swab inside the testing well
- Add the liquid testing solution
- Wait for 15 minutes to get a result
 In comparison to PCR tests these are less accurate.
 Advantage-
- Testing can be done outside the laboratory.
- Can be performed by the general public.
- Comparatively inexpensive.

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PCR reaction (RT PCR Test - Reverse Transcription-Polymerase Chain Reaction)


 It is a technique that takes specific sequence of DNA of small amount and amplifies it to be used for further
testing. It uses enzyme DNA polymerase (enzymes that make the copies of DNA) to synthesize new strands of
DNA.
 ARS–COV–2 is RNA virus. RNA is single-stranded & very unstable, which makes it difficult to work with. So
the viral RNA needs to be converted into DNA. This process is called Reverse Transcription (RT).

 Advantages-
- Small amount of DNA is required
- Result is obtained quickly and accurately.
- Not necessary to use radioactive material.
- Can be used to detect point mutations.

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